LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 3d metal shear simulation

units		metal
boundary	s s p

atom_style	atomic
lattice		fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region		box block 0 16.0 0 10.0 0 2.828427
create_box	3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
  2 by 2 by 1 MPI processor grid

lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 		origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms	1 box
Created 1912 atoms
  Time spent = 0.000400543 secs

pair_style	eam
pair_coeff	* * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11

neighbor	0.3 bin
neigh_modify	delay 5

region		lower block INF INF INF 0.9 INF INF
region		upper block INF INF 6.1 INF INF INF
group		lower region lower
264 atoms in group lower
group		upper region upper
264 atoms in group upper
group		boundary union lower upper
528 atoms in group boundary
group		mobile subtract all boundary
1384 atoms in group mobile

set		group lower type 2
  264 settings made for type
set		group upper type 3
  264 settings made for type

# void

region		void cylinder z 8 3.535534 2.5 INF INF
delete_atoms	region void
Deleted 204 atoms, new total = 1708

# temp controllers

compute		new3d mobile temp
compute		new2d mobile temp/partial 0 1 1

# equilibrate

velocity	mobile create 300.0 5812775 temp new3d
fix		1 all nve
fix		2 boundary setforce 0.0 0.0 0.0

fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify	3 temp new3d

thermo		25
thermo_modify	temp new3d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

timestep	0.001
run		100
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.1
  ghost atom cutoff = 5.1
  binsize = 2.55, bins = 23 14 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair eam, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          300   -7358.6159            0   -7312.8966   -9600.8353     19547.02 
      25    220.57465   -7320.4003            0   -7286.7852    832.69858     19547.02 
      50          300   -7292.1121            0   -7246.3928    7101.9213    19686.075 
      75     295.2793   -7286.9013            0   -7241.9014    5282.1114     19746.39 
     100          300   -7301.0026            0   -7255.2833   -1939.7714    19790.975 
Loop time of 0.0688287 on 4 procs for 100 steps with 1708 atoms

Performance: 125.529 ns/day, 0.191 hours/ns, 1452.882 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.059247   | 0.060771   | 0.062449   |   0.5 | 88.29
Neigh   | 0.0022693  | 0.0023552  | 0.0024772  |   0.2 |  3.42
Comm    | 0.0018966  | 0.0037905  | 0.005276   |   2.1 |  5.51
Output  | 8.297e-05  | 0.00011259 | 0.00019741 |   0.0 |  0.16
Modify  | 0.00082994 | 0.00084907 | 0.00086927 |   0.0 |  1.23
Other   |            | 0.0009506  |            |       |  1.38

Nlocal:    427 ave 437 max 419 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost:    780 ave 788 max 774 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs:    9859.75 ave 10248 max 9544 min
Histogram: 1 0 1 0 0 1 0 0 0 1

Total # of neighbors = 39439
Ave neighs/atom = 23.0907
Neighbor list builds = 4
Dangerous builds = 0

# shear

velocity	upper set 1.0 0 0
velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes

unfix		3
fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify	3 temp new2d

#dump		1 all atom 100 dump.shear.void

#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify	2 pad 4

#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify	3 pad 4

thermo		100
thermo_modify	temp new2d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

reset_timestep	0
run		3000
Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0    298.93143   -7301.0026            0   -7270.6316   -2766.8643    19799.958 
     100    301.13545   -7308.1131            0   -7277.5182   -8902.3332    19851.054 
     200    296.29577   -7306.2042            0    -7276.101   -9974.9354    19977.713 
     300    301.05914   -7303.6788            0   -7273.0916   -9862.4944      20024.1 
     400     303.0153    -7299.731            0   -7268.9451   -7947.0168    20095.075 
     500    298.65447   -7297.2717            0   -7266.9288   -5763.5283    20168.398 
     600    296.11526   -7292.6719            0   -7262.5871   -1784.5157     20265.23 
     700    305.84406   -7287.3611            0   -7256.2878   -1047.7333    20413.775 
     800    297.24737   -7280.1938            0   -7249.9939   -1482.5729    20516.847 
     900    305.15166   -7272.5442            0   -7241.5412   -806.41836     20629.22 
    1000    303.27519   -7264.3603            0    -7233.548   -2138.7382    20763.579 
    1100    297.64923   -7258.2644            0   -7228.0237   -768.39318    20890.609 
    1200    309.57038   -7254.7251            0   -7223.2732     826.2357    20995.654 
    1300          300   -7251.8391            0   -7221.3595    -1913.381    21121.462 
    1400          300   -7258.6892            0   -7228.2096   -5149.1767    21253.378 
    1500    304.55119   -7269.4714            0   -7238.5294   -8459.0382    21376.744 
    1600    302.21492   -7270.4103            0   -7239.7057   -10281.182    21489.117 
    1700          300   -7273.5589            0   -7243.0794   -11327.559    21616.147 
    1800    306.43021   -7269.3385            0   -7238.2057   -14197.412    21741.956 
    1900    306.23041   -7271.5332            0   -7240.4207   -19223.302    21854.329 
    2000    302.23263    -7267.091            0   -7236.3847   -20191.798    21975.252 
    2100    308.71627   -7268.4269            0   -7237.0618    -25282.39    22097.397 
    2200    306.77342   -7266.6664            0   -7235.4987    -27060.48    22230.534 
    2300          300   -7262.0978            0   -7231.6182   -24060.909    22351.457 
    2400          300   -7261.4125            0   -7230.9329   -20517.199    22462.608 
    2500    300.21813   -7260.6381            0   -7230.1364   -15407.463    22589.639 
    2600    296.24006   -7257.2142            0   -7227.1167    -13436.36    22711.783 
    2700          300   -7256.4647            0   -7225.9852    -15922.92    22830.263 
    2800    298.94765   -7255.6331            0   -7225.2605   -20555.015    22959.736 
    2900    294.98551   -7249.0201            0     -7219.05   -23986.374    23079.438 
    3000    291.21483   -7244.1837            0   -7214.5967   -25356.925    23197.918 
Loop time of 2.21357 on 4 procs for 3000 steps with 1708 atoms

Performance: 117.096 ns/day, 0.205 hours/ns, 1355.278 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.8072     | 1.86       | 1.9192     |   3.7 | 84.03
Neigh   | 0.11667    | 0.12264    | 0.13213    |   1.7 |  5.54
Comm    | 0.10804    | 0.17878    | 0.23557    |  13.3 |  8.08
Output  | 0.00073075 | 0.0012527  | 0.002811   |   2.5 |  0.06
Modify  | 0.024781   | 0.025831   | 0.02754    |   0.7 |  1.17
Other   |            | 0.02508    |            |       |  1.13

Nlocal:    427 ave 450 max 403 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost:    785.25 ave 844 max 723 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs:    9581.25 ave 10185 max 9102 min
Histogram: 2 0 0 0 0 0 0 1 0 1

Total # of neighbors = 38325
Ave neighs/atom = 22.4385
Neighbor list builds = 215
Dangerous builds = 0
Total wall time: 0:00:02
